title: Profiling of microRNA in human and mouse ES and iPS cells reveals overlapping but distinct microRNA expression patterns.
abstract: Using quantitative PCR-based miRNA arrays, we comprehensively analyzed the expression profiles of miRNAs in human and mouse embryonic stem (ES), induced pluripotent stem (iPS), and somatic cells. Immature pluripotent cells were purified using SSEA-1 or SSEA-4 and were used for miRNA profiling. Hierarchical clustering and consensus clustering by nonnegative matrix factorization showed two major clusters, human ES/iPS cells and other cell groups, as previously reported. Principal components analysis (PCA) to identify miRNAs that segregate in these two groups identified miR-187, 299-3p, 499-5p, 628-5p, and 888 as new miRNAs that specifically characterize human ES/iPS cells. Detailed direct comparisons of miRNA expression levels in human ES and iPS cells showed that several miRNAs included in the chromosome 19 miRNA cluster were more strongly expressed in iPS cells than in ES cells. Similar analysis was conducted with mouse ES/iPS cells and somatic cells, and several miRNAs that had not been reported to be expressed in mouse ES/iPS cells were suggested to be ES/iPS cell-specific miRNAs by PCA. Comparison of the average expression levels of miRNAs in ES/iPS cells in humans and mice showed quite similar expression patterns of human/mouse miRNAs. However, several mouse- or human-specific miRNAs are ranked as high expressers. Time course tracing of miRNA levels during embryoid body formation revealed drastic and different patterns of changes in their levels. In summary, our miRNA expression profiling encompassing human and mouse ES and iPS cells gave various perspectives in understanding the miRNA core regulatory networks regulating pluripotent cells characteristics.
authors.affiliation: Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors.forename: Siti Razila Abdul
authors.initials: SR
authors.lastname: Razak
authors.forename: Kazuko
authors.initials: K
authors.lastname: Ueno
authors.forename: Naoya
authors.initials: N
authors.lastname: Takayama
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Rika
authors.initials: R
authors.lastname: Saito
authors.forename: Hideto
authors.initials: H
authors.lastname: Koso
authors.forename: Chen-Yi
authors.initials: CY
authors.lastname: Lai
authors.forename: Miyako
authors.initials: M
authors.lastname: Murakami
authors.forename: Koichiro
authors.initials: K
authors.lastname: Tsuji
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Michiue
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Nakauchi
authors.forename: Makoto
authors.initials: M
authors.lastname: Otsu
authors.forename: Sumiko
authors.initials: S
authors.lastname: Watanabe
mesh_terms: D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D053595:Embryonic Stem Cells / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D016133:Polymerase Chain Reaction; D025341:Principal Component Analysis
chemical_list: D035683:MicroRNAs